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<title>singleTCW Instructions</title>
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<h2>Instructions</h2>
Terminology:
<ul>
<li><i>Sequence:</i> The input may be assembled transcripts, proteins or genes.  
<li><i>AnnoDB:</i> A database in FASTA format against which the sequences are blasted against
for annotation.
<li><i>DB hit:</i> An alignment of an entry from an annoDB (e.g. UniProt) to an sequence, i.e. 
an entry in the Blast result file. A given
sequence can 'hit' an annoDB multiple times (have alignments to multiple entries) and
it can 'hit' multiple different annoDBs (have alignments in more than one annoDB). 
<li><i>Best Anno:</i>From a list sorted on e-value, the first one with informative
annotation, which is any description that does not contain 
phrases such as "uncharacterized protein" (see 'Select Columns' Help for a more complete
description).
<li><i>Best Eval:</i> The hit with the best BLAST e-value; however, this may not be exactly 
the best e-value hit as if there is one almost as good that has informative annotation,
it will be used. 
</ul>
A few general rules:
<ol>
<li>
Selecting a label on the left results in a table, menu or sequence being displayed on
the right.
<li>There are two types of tables: Sequence and Pairs. NOTE: if sequence pairs were not calculated, the 
Pairs section will not be available.
<li>Columns can be changed for both the Sequence table and Pairs table:
<ol type="i">
<li><i>Important:</i> For both types of tables, the columns are not automatically changed
to match the filters; you must do that manually with the "Columns" for sequences or "Pairs Columns" for pairs.
<li>Columns within the table can be sorted by selecting the column heading (left mouse - ascending, right mouse - descending). The columns can be moved by dragging them.
<li>The columns viewed are saved (i.e. the next time you view the table, you will see the same columns). However,
the sorting and dragging of columns is not saved. Note: the columns are saved based
on the database name (hence, if two people are viewing the same database at the
same time, one person's column changes will effect the other person's tables).
</li>
</ol>
</ol>
<hr>
Detailed Help is provided on each page; the following provides an overview
of what is available.
<h3>Sequences</h3>

<b>&gt;&gt;Show All</b> - A table of all sequences in the database. 
<ul>
<li>To view a sequence from the table, select the sequence and then "View Selected Sequence".
<li>Change the columns in the table using "Select Sequence Columns".
</ul>

<b>&gt;&gt;Columns</b> - Menu of columns for the sequence table.
<ul>
<li>Select or deselect columns.
<li>The columns are not immediately changed for existing tables. Either select "Refresh All Existing Tables"
or redisplay the table (listed on the left panel) and select "Refresh columns".
</ul>

<b>&gt;&gt;Filters</b> - A menu with specific filters for sequences.
<ul>
<li>Select one or more filters, then select "View Filtered Sequences". The sequences that pass all filters will
be displayed in a table. 
<li>If you are not seeing the columns you desire, go to the "Select Sequence Columns", change
the columns, come back to the table (it will be listed on the left), and click "Refresh Columns".
</ul>

<b>&gt;&gt;Results</b> - List all Filter query results.
<ul>
<li>All queries that have been performed will be listed under this label. 
<li>Selecting a label will redisplay it on the right.
<li>To remove a label, select the 'x' beside it.
<li>If you select the "List Queries" label, it will show a table of what queries have
been run.
</ul>

<h3>Basic Queries</h3>
<b>&gt;&gt;Sequences</b> - Search on Seq ID,
Contig Notes or Read Names.  
<ul>
<li> 
This builds a table from searches performed.
<li>The resulting sequences can be shown as ""View Selected Sequence". 
<li>Columns can be changed with "Select Columns". 

</ul>

<b>&gt;&gt;annoDB Hits</b> - Search on the DB Id (e.g. UniProt ID) or description. 
<ul>
<li>It works like the basic Sequences.
</ul>

<b>&gt;&gt;GO Annotations</b> - Search on the GO Id or description. 
<ul>
<li>It works like the basic Sequences.
</ul>
<b>&gt;&gt;Blast</b> - Blast a sequence against all sequences in the database. 


<hr>
<h3>Similar Sequence Pairs</h3>
<ul>
<li>All options are the same as above, except apply to sequence pairs. 
<li>If there are no pairs, there will not be any labels under this section label.
</ul>
<i>View Selected Pair</i>
<ul>
<li>The alignment will be shown as nucleotide and amino acid sequences. 
</ul>  
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